repertoires of the nucleosome-positioning dinucleotides体验的nucleosome-positioning二核苷酸.pdfVIP

Repertoires of the Nucleosome-Positioning Dinucleotides 1 2,3 Thomas Bettecken *, Edward N. Trifonov 1 CAGT – Center for Applied Genotyping, Max Planck Institute of Psychiatry, Munich, Germany, 2 Genome Diversity Center, Institute of Evolution, University of Haifa, Haifa, Israel, 3 Division of Functional Genomics and Proteomics, Faculty of Science, Masaryk University, Brno, Czech Republic Abstract It is generally accepted that the organization of eukaryotic DNA into chromatin is strongly governed by a code inherent in the genomic DNA sequence. This code, as well as other codes, is superposed on the triplets coding for amino acids. The history of the chromatin code started three decades ago with the discovery of the periodic appearance of certain dinucleotides, with AA/TT and RR/YY giving the strongest signals, all with a period of 10.4 bases. Every base-pair stack in the DNA duplex has specific deformation properties, thus favoring DNA bending in a specific direction. The appearance of the corresponding dinucleotide at the distance 10.4 xn bases will facilitate DNA bending in that direction, which corresponds to the minimum energy of DNA folding in the nucleosome. We have analyzed the periodic appearances of all 16 dinucleotides in the genomes of thirteen different eukaryotic organisms. Our data show that a large variety of dinucleotides (if not all) are, apparently, contributing to the nucleosome positioning code. The choice of the periodical dinucleotides differs considerably from one organism to another. Among other 10.4 base periodicities, a strong and very regular 10.4 base signal was observed for CG dinucleotides in the genome of the honey bee A. mellifera. Also, the dinucleotide CG appears as the only periodical component in the human genome. This obs